JBrowse 1.10.10 released

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JBrowse 1.10.10 released

Robert Buels-2
Hi all,

JBrowse 1.10.10 has been released, with new compression support in
generate-names.pl, configurable inter-track spacing, and quite a few bug
fixes.

It can be downloaded from http://jbrowse.org/jbrowse-1-10-10.


# Release 1.10.10     2013-11-21 09:31:53 EST5EDT

## Minor improvements

  * Spacing between tracks is now configurable by setting
    `view.trackPadding` in the configuration.  Thanks to Chenchen Zhu
    for suggesting this (issue #377).

  * If reference sequences are defined, but no tracks are yet added,
    JBrowse will start normally instead of going to the
    "Congratulations, JBrowse is on the web" page.

  * `generate-names.pl` now supports a `--compress` option that
    compresses the name index files to save server disk space.  Thanks
    to Richard Hayes for pointing out the need for this (issue #378).

## Bug fixes

  * `generate-names.pl` now uses IO::Uncompress::Gunzip instead of
    PerlIO::gzip to read compressed VCF files.  This fixes a bug in
    which only the first few hundred names in a VCF were indexed.
    Thanks to Cris Lawrence for pointing this out (issue #380).

  * Fixed a bug in which `generate-names.pl` would crash if run with
    `--incremental` and no existing names index.  Thanks to Richard
    Hayes for pointing this out (issue #379).

  * Fixed a bug in which `generate-names.pl` would sometimes choose the
    wrong number of hash bits when performing incremental updates,
    leading to the old data being lost.  Thanks to Richard Hayes for
    lots of help troubleshooting this.

  * Fixed bug where other tracks are visible underneath pinned tracks
    when the display is scrolled down.  Thanks to Ed Lee for pointing
    this out.

  * Fixed a bug in which tooltip does not hide after the mouse leaves a
    Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for
    pointing this out.

  * Fixed a bug in which the `main.css` file for plugins was not being
    correctly loaded in some installations.  Thanks to Matt Bomhoff for
    pointing this out.



Happy browsing.  ;-)

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org